[ENH] clinica_pipeline decorator (#790)

* Basic implementation of clinica_pipeline decorator

* Propagate to all pipelines

* Add Pydra-pet-volume after rebasing

clinica/pipelines/__init__.py

@@ -1,3 +1,4 @@
+from ..pydra.pet_volume import pet_volume_cli as pydra_pet_volume_cli  # noqa
 from ..pydra.t1_linear import t1_linear_cli as pydra_t1_linear_cli  # noqa
 from ..pydra.t1_volume.create_dartel import cli as pydra_t1vol_cd_cli  # noqa
 from ..pydra.t1_volume.tissue_segmentation import cli as pydra_t1vol_ts_cli  # noqa

clinica/pipelines/deeplearning_prepare_data/deeplearning_prepare_data_cli.py

@@ -1,8 +1,9 @@
 import click
 
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 
+@clinica_pipeline
 @click.command(
     "deeplearning-prepare-data",
     deprecated=True,
@@ -18,6 +19,3 @@ def cli(*args, **kwargs):
         "\n\n"
         "See: https://clinicadl.readthedocs.io/en/stable/Preprocessing/Extract/"
     )
-
-
-run_cli.add_command(cli)

clinica/pipelines/dwi_connectome/dwi_connectome_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "dwi-connectome"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.caps_directory
 @cli_param.option_group.pipeline_specific_options
@@ -62,7 +63,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/dwi_dti/dwi_dti_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "dwi-dti"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.caps_directory
 @cli_param.option_group.common_pipelines_options
@@ -49,7 +50,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/dwi_preprocessing_using_fmap/dwi_preprocessing_using_phasediff_fmap_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "dwi-preprocessing-using-phasediff-fmap"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.bids_directory
 @cli_param.argument.caps_directory
@@ -69,7 +70,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "dwi-preprocessing-using-t1"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.bids_directory
 @cli_param.argument.caps_directory
@@ -70,7 +71,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/engine.py

@@ -10,6 +10,20 @@
 from nipype.pipeline.engine import Workflow
 
 
+def clinica_pipeline(func):
+    """Turns a CLI implementation into a Clinica Pipeline.
+
+    More precisely, this decorator takes care of:
+        - registering the implemented command as a subcommand
+          of `clinica run`.
+    """
+    from clinica.pipelines.cli import cli as run_cli
+
+    run_cli.add_command(func)
+
+    return func
+
+
 def postset(attribute, value):
     """Sets the attribute of an object after the execution.
 

clinica/pipelines/machine_learning/classification_cli.py

@@ -3,12 +3,13 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 from clinica.utils.atlas import T1_VOLUME_ATLASES
 
 pipeline_name = "machinelearning-classification"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.caps_directory
 @cli_param.argument.group_label
@@ -228,7 +229,5 @@ def cli(
     pipeline.run()
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/machine_learning_spatial_svm/spatial_svm_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "machinelearning-prepare-spatial-svm"
 
 
+@clinica_pipeline
 @click.command(pipeline_name)
 @cli_param.argument.caps_directory
 @cli_param.argument.group_label
@@ -106,7 +107,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/pet_linear/pet_linear_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "pet-linear"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.bids_directory
 @cli_param.argument.caps_directory
@@ -86,8 +87,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/pet_surface/pet_surface_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "pet-surface"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.bids_directory
 @cli_param.argument.caps_directory
@@ -79,7 +80,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/pet_surface/pet_surface_longitudinal_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "pet-surface-longitudinal"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.bids_directory
 @cli_param.argument.caps_directory
@@ -79,7 +80,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/pet_volume/pet_volume_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "pet-volume"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.bids_directory
 @cli_param.argument.caps_directory
@@ -123,8 +124,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/statistics_surface/statistics_surface_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "statistics-surface"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.caps_directory
 @cli_param.argument.group_label
@@ -198,7 +199,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/statistics_volume/statistics_volume_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "statistics-volume"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.caps_directory
 @cli_param.argument.group_label
@@ -165,7 +166,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/statistics_volume_correction/statistics_volume_correction_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "statistics-volume-correction"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.caps_directory
 @click.argument("t_map", type=click.Path(exists=True, resolve_path=True))
@@ -90,7 +91,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/t1_freesurfer/t1_freesurfer_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "t1-freesurfer"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.bids_directory
 @cli_param.argument.caps_directory
@@ -86,7 +87,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/t1_freesurfer_longitudinal/t1_freesurfer_longitudinal_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "t1-freesurfer-longitudinal"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.caps_directory
 @cli_param.option_group.common_pipelines_options
@@ -77,7 +78,5 @@ def cli(
     )
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()

clinica/pipelines/t1_freesurfer_longitudinal/t1_freesurfer_longitudinal_correction_cli.py

@@ -3,11 +3,12 @@
 import click
 
 from clinica.pipelines import cli_param
-from clinica.pipelines.cli import cli as run_cli
+from clinica.pipelines.engine import clinica_pipeline
 
 pipeline_name = "t1-freesurfer-longitudinal-correction"
 
 
+@clinica_pipeline
 @click.command(name=pipeline_name)
 @cli_param.argument.caps_directory
 @cli_param.option_group.common_pipelines_options
@@ -67,7 +68,5 @@ def cli(
         )
 
 
-run_cli.add_command(cli)
-
 if __name__ == "__main__":
     cli()